Warkton Tornado No.1 wrote:If the noise disappears with clutch pulled in & gears engaged, then the problem is most likely within the gearbox area.
My suspicions would be:
something is catching on the first gear or the inner clutch top plate (typically the kickstart) or;
the gears are noisy through too much clearance, a mismatch of gears or a broken tooth/teeth.
Strip down seems inevitable & I would suggest that you have a new, really thick chain case gasket & a selection of gearbox shims to hand as that may be all that it takes to cure it.
Sorry if I've missed it, but I can't find any mention of you having checked that the inner clutch top plate (pressure plate) or any part of the clutch is rubbing on the kickstart. Ideally, the pressure plate should look like new, not like an old 45 RPM record.
If it isn't that & you have the correct shimming to give as close to 0.003" as is possible, & the gears are not missing any teeth, then you should check the only things likely I believe to be remaining, which are mismatched gears (Sticky's book has number of teeth & outside diameter), a bad endplate bearing/journal/lay-shaft journal or the cursor itself.